AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
We present a WWW server for AUGUSTUS, a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model, a probabilistic model of a sequence and its gene structure. The web server allows the user to impose constraints on the predicted gene structure. A...
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Published in | Nucleic acids research Vol. 33; no. suppl-2; pp. W465 - W467 |
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Main Authors | , |
Format | Journal Article |
Language | English |
Published |
England
Oxford University Press
01.07.2005
Oxford Publishing Limited (England) |
Subjects | |
Online Access | Get full text |
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Summary: | We present a WWW server for AUGUSTUS, a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model, a probabilistic model of a sequence and its gene structure. The web server allows the user to impose constraints on the predicted gene structure. A constraint can specify the position of a splice site, a translation initiation site or a stop codon. Furthermore, it is possible to specify the position of known exons and intervals that are known to be exonic or intronic sequence. The number of constraints is arbitrary and constraints can be combined in order to pin down larger parts of the predicted gene structure. The result then is the most likely gene structure that complies with all given user constraints, if such a gene structure exists. The specification of constraints is useful when part of the gene structure is known, e.g. by expressed sequence tag or protein sequence alignments, or if the user wants to change the default prediction. The web interface and the downloadable stand-alone program are available free of charge at http://augustus.gobics.de/submission. |
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Bibliography: | istex:DBCD0925C08DD2B3B1684F2D4BB385DD67312187 ark:/67375/HXZ-KB9H8PFK-K To whom correspondence should be addressed. Tel: +49 551 3914926; Fax: +49 551 3914929; Email: mstanke@gwdg.de local:gki458 ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Article-1 ObjectType-Feature-2 |
ISSN: | 0305-1048 1362-4962 |
DOI: | 10.1093/nar/gki458 |